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The Morphology of Complex Materials: MTEN 657

MWF 3:00-3:50 Baldwin 641Prof. Greg Beaucage

β-Sheetwebhost.bridgew.edu/fgorga/proteins/beta.htm

Aggregated Nanoparticlesfrom Lead Based Paint

“Emerging Issues in Nanoparticle Aerosol Science and Technology (NAST)”

NSF 2003

Course Requirements:

-Weekly Quiz (8 to 9 in quarter)-Comprehensive Final (worth 3

quizzes)

-Old Quizzes will serve as homework

(These have posted answers)I may also assign other homework

where it is needed

You can replace quiz grades with a (or several) report(s) on a topical

area not covered in class but pertaining to the hierarchy of

morphology for a complex material. Several examples are given on the

web page.

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Structural Hierarchy of Complex Materials

Consider that we would like to understand a forest, such as the Amazon Forestfrom a Structural Perspective in order to develop predictive capabilities and an understanding

of the basic features to such a complex structure.

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Structural Hierarchy of Complex Materials

Consider that we would like to understand a forest, such as the Amazon Forestfrom a Structural Perspective in order to develop predictive capabilities and an understanding

of the basic features to such a complex structure.

http://www.eng.uc.edu/~gbeaucag/Classes/MorphologyofComplexMaterials/Overview.html

1) The first logical step is to consider a base (primary) unit for the forest and

2) then devise a repetition or branching rule (fractal scaling law) to create trees (secondary structure).

We revise the scaling rules and primary unit until we produce the type of trees we are interested in.

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Structural Hierarchy of Complex Materials

Consider that we would like to understand a forest, such as the Amazon Forestfrom a Structural Perspective in order to develop predictive capabilities and an understanding

of the basic features to such a complex structure.

http://www.eng.uc.edu/~gbeaucag/Classes/MorphologyofComplexMaterials/Overview.html

We could consider other types of trees in the same way.

3) Trees form clusters or groves (tertiary structure) that can follow a spacing and shape rule, for instance, redwoods grow in “fairy” rings or “cathedral” groups

around an old tree.

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Structural Hierarchy of Complex Materials

Consider that we would like to understand a forest, such as the Amazon Forestfrom a Structural Perspective in order to develop predictive capabilities and an understanding

of the basic features to such a complex structure.

4) Groupings of groves of trees interact with the environment to form forests (quaternary structures)

5) Higher levels of organization can be considered

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Structural Hierarchy of Complex Materials

-We have considered discrete “levels” of structure within a hierarchical model.

-In constructing the hierarchy is it natural to start from the smallest scale and to build up.

-We have borrowed from proteins in labeling the hierarchical levels primary, secondary, tertiary and quaternary.

-The hierarchical approach gives insight into how complex natural systems can be understood as if the structural levels acted independently in some respects.

-One of the main insights from hierarchical models is to understand in detail how and why structural levels are not independent and how they can interact to

accommodate the environment.

-In this course we will consider the application of hierarchical models to understand complex molecular systems with the goal of understanding how the hierarchical

approach can be expanded.

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Topics we will cover:

1) Protein structure (the origin of the hierarchical concept) 3 weeks

2) DNA and RNA structure (first adaptation of the hierarchical approach)1 week

3) Polymer Chain Structure in Solution (a statistical hierarchy) 2 weeks

4) Hierarchy of Polymer Dynamics in Solution (a kinetic hierarchy) 1 week

5) Polymer Crystalline Structure (hierarchy in a structural material) 2 weeks

6) Branched Fractal Aggregates (hierarchy in a statistical structural material)1 week

Structural Hierarchy of Complex Materials

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Twig

Tree/Branching

Grove/Cluster

Structural Hierarchy of Complex Materials

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The StructuralHierarchy of Proteins

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Size of proteins.html

Four Levels of Protein Structure.html

http://learn.genetics.utah.edu/content/begin/cells/scale/

http://www.youtube.com/watch?v=y8Z48RoRxHg&feature=related

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http://www.friedli.com/herbs/phytochem/proteins.html#peptide_bond

The α-carbon is a chiral centerit is always in an L-configuration spelling “CORN” in the Newman projection

There are 20 choices for the “R” group in nature. This makes an alphabet from which sequences of these 20 letters can code for any protein. Depending on the chemical functionality of the “R” groups different properties, polarity, hydrophobicity, ability to bond by disulfide linkages, hydrogen bonding and chain flexibility or rigidity can be imparted to the protein.

Quick Look at Amino Acids.htmlhttp://www.johnkyrk.com/aminoacid.html

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Amino Acids.html

3D Amino Acids

http://www.bioscience.org/urllists/aminacid.htm

http://www.mcb.ucdavis.edu/courses/bis102/Polar.html

More Amino Acidshttp://biology.clc.uc.edu/courses/bio104/protein.htm

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Methionine Start Amino Acid (usually removed in later steps)

Glycine -H Flexible non-polarAlanine -CH3 Flexible non-polar

Proline 10-40% Cis Configuration depending on neighboring amino acid residues Found in Turns and at start of α-helix

Cystine Disulfide Linkages (Hair is 5% cystine)

Hydrogen Bonding in Kevlar

NH = DonorC=O = Acceptor

Polyamides are similar to proteins

Know These 5 Amino Acids Well

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The Genetic Code Links.html

Post Translational Modification

of Insulin

Movie of Protein Synthesishttp://nutrition.jbpub.com/resources/animations.cfm?id=14&debug=0

http://www.eng.uc.edu/~gbeaucag/Classes/MorphologyofComplexMaterials/GeneticCode.html

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The Peptide Bond

Resonance structures make the peptide group planar (like a card).

Proline is the exception Proline adds main chain curvature

found in turns and at start of α-helix

http://www.friedli.com/herbs/phytochem/proteins.html#peptide_bond

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The peptide linkage forms a planar structure with the two α-carbons and the N,

H, C and O atoms

PSI ψ is the rotation angle between the carboxyl C and the α-carbon

PHI Φ is the rotation angle between N and the α-carbon

Certain values of these two rotation angles are preferred in certain structures

So the angles serve as a map for the protein secondary structure

http://www.friedli.com/herbs/phytochem/proteins.html#peptide_bond

Fully Extended Chain (Planar Zig-Zag)Phi/Psi 180, 180

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http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html

http://visu.uwlax.edu/BioChem/Rotate.mov Phi rotation for Psi = 0

Psi rotation for Phi = 0

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http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html

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Ramachandran Plots.html

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Folding Simple Dynamic Simulation.html

More Complicated Simulation.html

Yet more complicated.html

Where and When do Proteins Fold.html

Small Protein Folding.html

Another Small Protein Folding.html

Folding a Protein by Hand.html

Entropy and Protein Folding.html

Folding of Villin.html

Lets Jump Ahead and Look at Protein Folding

http://intro.bio.umb.edu/111-112/111F98Lect/folding.html

http://www.youtube.com/watch?v=_xF96sNWnK4&feature=related

http://www.cs.ucl.ac.uk/staff/D.Jones/t42morph.html

http://www.youtube.com/watch?v=meNEUTn9Atg

http://www.youtube.com/watch?v=BrUdCVwgJxc&feature=related

http://www.youtube.com/watch?v=E0TX3yMEZ8Y&feature=related

http://www.youtube.com/watch?v=va92d9Ei1QM&feature=related

http://www.youtube.com/watch?v=gaaiepNVyvE&feature=related

http://www.youtube.com/watch?v=1eSwDKZQpok&feature=related

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Secondary Structures of Proteinsα-Helix, β-Sheets, Turns

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pdb of α-Helixhttp://employees.csbsju.edu/hjakubowski/Jmol/alpha_helix/alpha_helix.htm

Right Handed α-Helix

http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html

C=O from residue “i”hydrogen bonds with

NH from residue “i+4”

Phi/Psi angles are -57, -47

Residues per turn = 3.6Rise per turn = 5.4 Å

Amino Acids and HelixGlycine too flexible

Proline too rigidShort H-Bonding (Ser, Asp, Asn) Disrupt Coil

Long H-Bonding are OKBranches at α-C Disrupt Coil (Val, Ile)

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http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html

Valine

Isoleucine

Serine

Asparagine

AsparticAcid

Glycine

Proline

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Other Types of Helices

310 helix

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β-Sheets

Phi PsiParallel -119 +113Anti-Parallel -139 +135α-Helix -57 -47Extended ±180 ±180

Rippled Sheets

H-Bonding between strands in SheetH-Bonding within strand in Helix

Parallel => 12 member ringsAnti-Parallel => 14 and 10 member rings alternating

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Parallel β-Sheets

12-member rings

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Anti-Parallel β-Sheets

Alternating 10- and 14-member rings

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Twisted β-Sheet/Saddle

Twisted β-Saddle

http://employees.csbsju.edu/hjakubowski/Jmol/Twisted%20Beta%20Sheet/Twisted_Beta_Sheet.htm

β-Barrel

β-Barrelhttp://employees.csbsju.edu/hjakubowski/Jmol/beta_barrel_tpi/Beta_Barrel_tpi.htm

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http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html

Valine

Isoleucine

Serine

Asparagine

AsparticAcid

Glycine

Proline

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β-Turns

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β-Turns

Reverse Turnhttp://employees.csbsju.edu/hjakubowski/Jmol/RevTurnTryInhib/revturnTrpInhib.htm

Type 2 and Type 1 Reverse Turns

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Micelles (Vesicle)

Dodecylphosphocholine (DPC) Micelle

http://employees.csbsju.edu/hjakubowski/Jmol/Micelle/micelle.htm

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Protein with a buried hydrophobic grouphttp://employees.csbsju.edu/hjakubowski/Jmol/HAAPBJmol/HAAPBBovineBuryF10.htm

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~50% of amino acids are in well defined secondary structures27% in α-helix and 23% in β-sheets

Native state proteins have a packing density slightly higher than FCC/HCP 0.75 vs 0.74

Organic liquids 0.6-0.7 Synthetic Polymer Chain in Solution ~0.001 So the transition from an unfolded protein in solution to a native state protein

involves a densification of about 750 to 1000 times.

Nonpolar 83% internal, Charged 54% exposed, uncharged 63% internal

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Super-Secondary Structures

Common motifs

Helix-Loop-Helix

EF-Hand

http://employees.csbsju.edu/hjakubowski/Jmol/Lambda_Repressor/Lambda_Repressor.htm

http://employees.csbsju.edu/hjakubowski/Jmol/Calmodulin_EF_Hand/Calmodulin_EF_Hand.htm

DNA and Calcium Binding sites

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β-Hairpin or Beta-Beta in Anti-Parallel Structures

Super-Secondary Structures

http://employees.csbsju.edu/hjakubowski/Jmol/Bovine%20Pancreatic%20Trypsin%20Inhibitor/Bovine_Pancreatic_Trypsin_Inhibitor.htm

Greek Key Motif

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Beta-Alpha-Beta (to connect two parallel β-sheets)http://employees.csbsju.edu/hjakubowski/Jmol/BETA-ALPHA-BETA_MOTIFF/BETA-ALPHA-BETA_MOTIFF.htm

β-Helicieshttp://cti.itc.virginia.edu/~cmg/Demo/pdb/ap/ap.htm

(seen in pathogens, viruses, bacteria)

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Many β-Topologies

http://www.cryst.bbk.ac.uk/PPS2/course/section10/all_beta.html

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3 Classes of Proteins (Characteristic Secondary Structures)

α-Proteins

αβ-Proteins

β-Proteins

Cytochrome B562http://employees.csbsju.edu/hjakubowski/Jmol/Cytochrome_B562/Cytochrome_B562.htm

Met-Myoglobinhttp://employees.csbsju.edu/hjakubowski/Jmol/Met-Myoglobin

Triose Phosphate Isomerasehttp://employees.csbsju.edu/hjakubowski/Jmol/Triose%20Phosphate%20Isomerase/TRIOSE_PHOSPHATE_ISOMERASE.htm

Hexokinasehttp://employees.csbsju.edu/hjakubowski/Jmol/Hexokinase/HEXOKINASE.htm

Superoxide Dismutasehttp://employees.csbsju.edu/hjakubowski/Jmol/Superoxide%20Dismutase/SUPEROXIDE_DISMUTASE.htm

Human IgG1 Antibodyhttp://employees.csbsju.edu/hjakubowski/Jmol/Human%20Antibody%20Molecule-IgG1/Human_Antibody_Molecule%C2%AD_IgG1.htm

Retinol Binding Proteinhttp://employees.csbsju.edu/hjakubowski/Jmol/Retinol%20Binding%20Protein/RETINOL_BINDING_PROTEIN.htm

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Fibrillar (elastic) versus Globular Proteins

Elastin (Blood Vessels) β-sheets and α-helicies with β-turns

Reslin (Insects Wings)

Silk (Spiders etc.) β-sheets and α-helicies with β-turns

Fibrillin (Cartilage) - Folded β-Sheet like and Accordian

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Tertiary Structure and Protein Folding

Consider a protein of 100 residues each with two bond angles Φ and ψ that can take 3 positions each so 9 conformations. The

chain has 9100 = 2.7 x 1095 conformations. Even with 10-13s to change a conformation, it

would take 8.4 x 1074 years to probe all conformations (that is along time).

Such a protein folds in less than a second. This is called Levinthal’s Paradox.

The key to resolving Levinthal’s Paradox is to limit the choices.

Disulfide bonds are a major limiting factor,Consider Ribonuclease (RNase A) (an enzyme that degrades RNA)

Having 4 disulfide bonds that serve as tethers for the folding process.

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Folds “like a taco” to bind with the RNA substrate

Armour purified 1 kilo and gave it away for study

124 residues 13.7 kDaPolycation that binds with polyanionic RNA

Positive charges are in the taco cleft.

RNase Ahttp://www.rcsb.org/pdb/explore/jmol.do?structureId=7RSA&bionumber=1

Nobel Prize Lecture published as:Anfinsen, C.B. (1973) "Principles that govern the folding of protein chains." Science

181 223-230.

Anfinsen Postulate: For Small Globular Proteins the Tertiary Structure is determined only by the

amino acid sequence

http://employees.csbsju.edu/hjakubowski/Jmol/RNase/RNase.htm

RNase Structure

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β-Mercapto Ethanol

Urea

Competes with H-BondsDenatures (Destablizes) Proteins

Competes with H-BondsDenatures (Destablizes) Proteins

Guanidine-HCl

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http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olprotfold.html

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http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olprotfold.html

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Native state is a “Global Minimum in Free Energy”Folding Process Occurs on an Energy “Funnel”

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Folding does not occur by a single pathway, but is a statistical processof searching the energy landscape for minima

For large proteins we see intermediates, molten globules, non-biologically active dense states

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Simple proteins undergo a cooperative process

y-axis could be viscosity (hydrodynamic radius),

circular dichroism, fluorescence,

diffusion coefficient (hydrodynamic radius) from dynamic light scattering,

radius of gyration from static light scattering

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Viscosity

Native state has the smallest volume

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Mass Fractal Dimension, 1 ≤ df ≤ 3

Mass ~ Size1

Mass ~ Size2

1-d df = 1

df = 22-d

Mass ~ Size3 df = 33-d

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Mass Fractal Dimension, 1 ≤ df ≤ 3

Mass ~ Size2

Mass ~ Size1.67

2-d df = 2

df = 5/3

Random (Brownian) Walkθ-Solvent Condition

Self-Avoiding Walk/Expanded CoilGood Solvent Condition

In the collapse transition from an expanded coil to a native state for a protein of 100 residues (N = Mass = 100)

Size ~ 15.8 for Expanded Coil (10 for Gaussian) and 4.6 for Native State

For N = 10000 this becomes 251 : 100 : 21.5For large proteins the change in size is dramatic (order of

10x)

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Viscosity

For the Native State Mass ~ ρ VMolecule

Einstein Equation (for Suspension of 3d Objects)

For “Gaussian” Chain Mass ~ Size2 ~ V2/3

V ~ Mass3/2

For “Expanded Coil” Mass ~ Size5/3 ~ V5/9

V ~ Mass9/5

For “Fractal” Mass ~ Sizedf ~ Vdf/3

V ~ Mass3/df

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Viscosity

For the Native State Mass ~ ρ VMolecule

Einstein Equation (for Suspension of 3d Objects)

For “Gaussian” Chain Mass ~ Size2 ~ V2/3

V ~ Mass3/2

For “Expanded Coil” Mass ~ Size5/3 ~ V5/9

V ~ Mass9/5

For “Fractal” Mass ~ Sizedf ~ Vdf/3

V ~ Mass3/df

“Size” is the“Hydrodynamic Size”

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Circular Dichroism

Light Polarizationhttp://www.enzim.hu/~szia/cddemo/edemo0.htm?CFID=1025184&CFTOKEN=88815524

CD Spectroscopy for Proteins

http://www.cryst.bbk.ac.uk/PPS2/course/section8/ss-960531_21.html

Wikipedia on CDhttp://en.wikipedia.org/wiki/Circular_dichroism

http://www.ruppweb.org/cd/cdtutorial.htm

Difference in Absorption

Molar Circular Dichroism (c = molar concentration)

Degrees of Ellipticity

These change with the extent and nature of secondary structure such as helicies

Examples of CDhttp://www.ap-lab.com/circular_dichroism.htm

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Static Light Scattering for Radius of Gyration

Guinier’s Law

Beaucage G J. Appl. Cryst. 28 717-728 (1995).

€

γGaussian r( ) = exp −3r2

2σ 2( )

σ 2 =

xi −μ( )2

i=1

N

∑N −1

= 2Rg2

€

I q( ) = IeNne2 exp

−Rg2q2

3 ⎛

⎝ ⎜

⎞

⎠ ⎟

Lead Term is

€

I(1/ r) ~ N r( )n r( )2

€

I(0) = Nne2

€

γ0 r( ) =1−S

4Vr +...

A particle with no surface

€

r⇒ 0 then d γGaussian r( )( )

dr⇒ 0

Consider binary interference at a distance “r” for a particle with arbitrary orientationRotate and translate a particle so that two points separated by r lie in the particle for all rotations

and average the structures at these different orientations

Binary AutocorrelationFunction

Scattered Intensity is the Fourier Transform ofThe Binary Autocorrelation Function

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For qRg >> 1

df = 2

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For static scattering p(r) is the binary spatial auto-correlation function

We can also consider correlations in time, binary temporal correlation functiong1(q,τ)

For dynamics we consider a single value of q or r and watch how the intensity changes with timeI(q,t)

We consider correlation between intensities separated by tWe need to subtract the constant intensity due to scattering at different size scales

and consider only the fluctuations at a given size scale, r or 2π/r = q

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Dynamic Light Scattering

a = RH = Hydrodynamic Radius

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Dynamic Light Scattering

http://www.eng.uc.edu/~gbeaucag/Classes/Physics/DLS.pdf

my DLS web page

Wikihttp://webcache.googleusercontent.com/search?q=cache:eY3xhiX117IJ:en.wikipedia.org/wiki/Dynamic_light_scattering+&cd=1&hl=en&ct=clnk&gl=us

Wiki Einstein Stokes

http://webcache.googleusercontent.com/search?q=cache:yZDPRbqZ1BIJ:en.wikipedia.org/wiki/Einstein_relation_(kinetic_theory)+&cd=1&hl=en&ct=clnk&gl=us

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Optical Tweezers

Dielectric particles are attracted to the center of a focused beamScattering Force moves particles downstream

Force can be controlled with intensity of laser

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Stretching of a single protein (RNase)

http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olprotfold.html

Blue: Stretch just DNA linker moleculesRed: Stretch DNA and ProteinGreen: Release tension on Protein/DNA

Link to Paper at Sciencehttp://www.sciencemag.org/content/309/5743/2057

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It's been estimated that over half of all native proteins have regions (greater than 30

amino acids) that are disordered, and upwards of 20% of proteins are completely

disordered.

Natively Unfolded Proteins

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Membrane Proteins

http://blanco.biomol.uci.edu/mp_assembly.html

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http://blanco.biomol.uci.edu/translocon_machinery.html

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http://www.portfolio.mvm.ed.ac.uk/studentwebs/session2/group5/introliz.htm

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Electron transport chain is part of the ATP/ADP energy generation pathway for cellsThis involves many tertiary protein structures. For instance, Complex III is a quaternary structureof 9 proteins.

Heme B group

Quaternary Structures

http://en.wikipedia.org/wiki/Electron_transport_chain

http://proteopedia.org/wiki/index.php/Complex_III_of_Electron_Transport_Chain

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Quaternary Structure Page

http://proteopedia.org/wiki/index.php/Main_Page

Ribosome

http://proteopedia.org/wiki/index.php/Ribosome

Poly(A) Polymerase

http://proteopedia.org/wiki/index.php/2q66

Ribosome in Actionhttp://www.youtube.com/watch?v=Jml8CFBWcDs

Role of Ribosome

http://www.cytochemistry.net/cell-biology/ribosome.htm

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DNA/Protein Quaternary Structureshttp://www.biochem.ucl.ac.uk/bsm/prot_dna/prot_dna_cover.html

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RNA structure

Ribose

http://www.rnabase.org/primer/

t-RNA (Folded Structure)Deoxyribose

DNA

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If it takes DNA/RNA to template a protein and proteins to make/control DNA/RNAWhich came first Proteins or Nucleic Acids?

RNA World Hypothesis:

http://en.wikipedia.org/wiki/RNA_world_hypothesis

http://exploringorigins.org/rna.html

L1 Ligase Ribozyme

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Hierarchy of a Chromosome

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Core Histone

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http://www.eng.uc.edu/~gbeaucag/Classes/MorphologyofComplexMaterials/Physics%20of%20Chromatin%20Schiessel%202003.pdf

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